Screening of the general population for subclinical atherosclerosis is controversial. We assessed the prevalence of subclinical atherosclerosis in healthy middle-aged individuals by 4 non-invasive modalities. In 277 randomly selected males (n = 121) and females (n = 156), aged 50 or 60 years, without known cardiovascular disease or diabetes, intima-media thickness/presence of carotid plaques by ultrasound; coronary artery calcification (CAC) by non-contrast enhanced cardiac CT; occurrence of peripheral artery disease (PAD) by ankle brachial index (ABI), and vascular leakage by urine albumin creatinine ratio (ACR), were evaluated. Traditional risk factors were obtained and HeartScore was calculated. A total of 56 % had morphological signs of atherosclerosis in one of the vascular territories; 41 % had CAC and 31 % a carotid plaque. Among individuals with atherosclerosis, 28 % had lesions in both vascular territories. Subclinical atherosclerosis was significantly more frequent in older males. Signs of PAD and microalbuminuria were very uncommon and detected in only 1 % of the entire population. No association was found between morphological signs of subclinical atherosclerosis and ABI or ACR. More than half of randomly selected apparently healthy middle aged individuals had subclinical atherosclerosis located in the coronary or carotid arteries.